Windows Installer doesn't support the concept of "Any CPU". MSI's are platform architecture specific. You need an x86 MSI and an x64 MSI. There are tricks around this (google Hybrid Installer) but you hit limitations here and there and end up writing custom actions that are not desirable.
If the console app is .NET compiled for Any CPU, I'd just treat it as 32bit software and install to ProgramFilesFolder (x86) and 32bit registry. It'll be installed as a 32bit app but it'll actually run as a 64bit process no problem. Just in your app code when you read the registry be sure to read from the 32bit hive to get your pid key.